The same dust off shot would work regardless of how you held your camera, horizontal versus vertical orientation.
If you do it the way you suggest you would likely need two correction frames. One taken with your camera in horizontal orientation and one in vertical. Then two batch operations, one to apply your horizontal corrections to horizontal shots, the other for vertical shots. You also stand the chance of correcting something important that didn't need it and just happens to be where the sky was supposed to be
If you can commit to turning off the camera's auto sensor cleaning feature, it's easy to always have a dust off file that works with whatever images you choose. Here's an example of what I do....
Day 1-use camera sensor cleaner manually, create a dust off ref photo Day 20-use camera sensor cleaner manually, create a dust off ref photo Day 40-use camera sensor cleaner manually, create a dust off ref photo
Put all the NDF ref photos in one folder, give it a name like DustOffRefs. Point CNX's dust off feature to that folder.
If today is Day 50, CNX will find a valid NDF file for every image shot since day 1.
The trick is to always clean & create the file at the same time. If, on day 30 I cleaned the sensor but neglected to create the ref file, CNX would not find a matching NDF file for photos I took between day 30 and 40.